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I think another solution would be having the perl modules installed using packaging tools on a different path. Like, adding another directory to Perl's @INC and let that be the place where dual-life modules live.

We must install dual-life modules in CORE in order for them to be loaded. Otherwise, if we install these modules in SITE, the old version in CORE will shadow the new version. That's what the UNINSTExtUtils::MakeMaker parameter is for (--uninstall for Module::Build). See for example CPAN-RT#22130 [cpan.org].